Covariance Method

1. Importing and declaring all the necessary variables

2. Generating Testing Data

Here, I removed gly from the testing data due to lacking of beta carbon chemical shift

##    AA    CA    CB
## 1 SER 59.84 63.59
## 2 THR 62.47 69.49
## 3 ASP 54.54 41.14
## 4 ASP 53.98 41.14
## 5 SER 58.76 63.31
## 6 PRO 64.81 31.54

3. Calculating the Frequence from testing data

##       AA  freq                 
##  [1,] "A" "0.0530973451327434" 
##  [2,] "R" "0.0442477876106195" 
##  [3,] "N" "0.0353982300884956" 
##  [4,] "D" "0.0973451327433628" 
##  [5,] "C" "0"                  
##  [6,] "Q" "0.0530973451327434" 
##  [7,] "E" "0.106194690265487"  
##  [8,] "H" "0.00884955752212389"
##  [9,] "I" "0.0353982300884956" 
## [10,] "L" "0.115044247787611"  
## [11,] "K" "0.0442477876106195" 
## [12,] "M" "0.0530973451327434" 
## [13,] "F" "0.0707964601769911" 
## [14,] "P" "0.0619469026548673" 
## [15,] "S" "0.0619469026548673" 
## [16,] "T" "0.0530973451327434" 
## [17,] "Y" "0.0265486725663717" 
## [18,] "W" "0"                  
## [19,] "V" "0.079646017699115"

4. Assembling the 5 different coveriance matrix

Method A: formularize covariance matrix with secondary structures.

\[Cov= \begin{pmatrix} Sd_{Ca} & cov \\ cov & Sd_{Cb} \end{pmatrix} \] For each amino acid there should be three covariance matrices. For example, Cystein (ox) Covariance Matrix for \(\alpha\)-helix Secondary Structure.

##          [,1]     [,2]
## [1,] 2.430000 1.987452
## [2,] 1.987452 2.790000

Method B: formularize covariance matrix with cov = 0 but differenciate the standard deviations among secondary structures.

\[Cov= \begin{pmatrix} Sd_{Ca} & 0 \\ 0 & Sd_{Cb} \end{pmatrix} \] There are 3 covariance matrices for each residue. For example, Arginine Covariance Matrix for \(\alpha\)-helix Secondary Structure

##      [,1] [,2]
## [1,] 2.43 0.00
## [2,] 0.00 2.79

Method C: use the average of coveriance from 3 different secondary structure to fill the matrix.

\[Cov= \begin{pmatrix} Sd_{Ca} & cov_{avg} \\ cov_{avg} & Sd_{Cb} \end{pmatrix} \]

First Calculate all the average covariance of all the amino acides
Then use the average of of the covariance fill the matrix

There should be three matrices for each amino acid.

For example, Arginine Covariance Matrix for \(\alpha\)-helix Secondary Structure

##           [,1]      [,2]
## [1,]  2.430000 -0.692594
## [2,] -0.692594  2.790000

Method D: Using covariance without scondary structure.

The standard deviation is the average standard deviation and the covariance is the average coveriance. \[Cov= \begin{pmatrix} Sd_{Ca, avg} & cov_{avg} \\ cov_{avg} & Sd_{Cb, avg} \end{pmatrix} \] For example, Arginine Covariance Matrix for any Secondary Structure

##           [,1]      [,2]
## [1,]  2.160000 -0.692594
## [2,] -0.692594  3.220000

Method E: Using the average of standard deviation and cov=0

Similar to Method D but with cov=0. For exam for arginine.

##      [,1] [,2]
## [1,] 2.16 0.00
## [2,] 0.00 3.22

Calculate all the covariance & inverse matrixfor method A-E

For example, for method A, Alanine covariance and inverse covariance matrix are:

##          [,1]     [,2]
## [1,] 2.430000 1.987452
## [2,] 1.987452 2.790000

##          [,1]     [,2]
## [1,] 0.462963 0.000000
## [2,] 0.000000 0.310559

5. Calculate the Probability

Calculating the \(\chi^{*}\)

Using the \(\chi^{*}\) to get corresponding Probability

6. Finding the sum of absolute value of the difference between predicted and observed.

Reference Correction Calculation Function, return the sum of absolute difference

7. Overall Testing Function

The last version return a correction -0.38. And this version return a correction of -2.220446e-16, which is really small, and the correct reference is 0.

## [1] "#################################### bmr10060.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] -0.1632653
## [1] "Method B"
## [1] -0.1020408
## [1] -0.08163265
## [1] "Method C"
## [1] -0.5102041
## [1] -0.2040816
## [1] "Method D"
## [1] -0.5102041
## [1] -0.4489796
## [1] "Method E"
## [1] -0.1020408
## [1] 0
## [1] "Method A:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBLHBHBYMWRMNBTKBBNSPTNLSVLEBBTWMNHAQDCHPDPPNQNBYVRSWTDQHYTQSFRPTBLBTLTTMPBDSTQTAPRRYBVHHSTVHPEHYCQRIAQMYMDLSCADNQTBLWFHRANHWYYDPAM"
## [1] "Method B:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBLQBCBFVWRMNBTKBBNTPTNLSVBEBBTWMDHAQDCQPDPVNQNBYVRSWTDQHYTQSFEPTDLBTLTTMPBDSTCTAVRMYIVHQSTVHPWHYCQRIAQMYMLLSCADNQTBLWFHRANEWYYDPAK"
## [1] "Method C:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "VVNVVVVVVVVVVVVVVVVVVVVNVVVCVVCVVVVVVVCVVVCVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVCVVVVVVVCVVVVVVVVVCVVVVVVVV"
## [1] "Method D:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "CRNCCCCCCCCCCCCRCNCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCCCQNCCCRCCCCQCCCCCCCCCCCCCCCCCCCCCCCCCCCMCCCCCCCCCCECCCCCCCCCCMCCCCCCCCCCCCCCCCCCCCCCCCC"
## [1] "Method E:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBFQBCYFVWRMNDTMBBNTPTNLSVLELBTWMNHAQDCQPDPVNQNBYVRSWTDQHYTQSFEVTDLBTLTTNPBDSTQTAVRMYIVHHSTVHVWHYCQRIAQMYMLLSCADNQTBLWFHKANEWYYDPAM"
## [1] "Total number of residues in original sequence is: 136"
## $Method_A
## $Method_A$`Match Sum`
## [1] 56
## 
## $Method_A$`Match Percentage`
## [1] 41.17647
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 59
## 
## $Method_B$`Match Percentage`
## [1] 43.38235
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 9
## 
## $Method_C$`Match Percentage`
## [1] 6.617647
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 6
## 
## $Method_D$`Match Percentage`
## [1] 4.411765
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 62
## 
## $Method_E$`Match Percentage`
## [1] 45.58824
## 
## 
## [1] "#################################### bmr10101.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] -0.122449
## [1] "Method B"
## [1] -0.1020408
## [1] -0.122449
## [1] "Method C"
## [1] 0.1020408
## [1] 0.122449
## [1] "Method D"
## [1] 0.1020408
## [1] 0.08163265
## [1] "Method E"
## [1] -0.1020408
## [1] -0.1632653
## [1] "Method A:"
## [1] "MSEVTRSLQRWALRRADDSWQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKTIKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTNKEPFDVPI"
## [1] "MSHPTWSLQHCALHRANFSHHIVCAIBEBQIFARRBQKCAHAQCNNSCBTWWQKTIRIATCLEBQSAABCSTQSQHEIMFEBLKMLCPILMNIYTNMQPLNMPI"
## [1] "Method B:"
## [1] "MSEVTRSLQRWALRRADDSWQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKTIKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTNKEPFDVPI"
## [1] "MSHPTWSLQHCALHRANFSHQBVCAIBEYQIBARRBQKCAQAQENNSCBTWWQKTIRIATCLWBCSAABHSTQSQHEBMFEBLKMDCPILKNIYTNMQPLNVPI"
## [1] "Method C:"
## [1] "MSEVTRSLQRWALRRADDSWQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKTIKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTNKEPFDVPI"
## [1] "VVVCVVVVVVVVVVVVCVVVVVCVVVVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVV"
## [1] "Method D:"
## [1] "MSEVTRSLQRWALRRADDSWQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKTIKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTNKEPFDVPI"
## [1] "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCNCCCNMCCCCCCC"
## [1] "Method E:"
## [1] "MSEVTRSLQRWALRRADDSWQLVEAIDEYQILARHLQKEAQAQHNNSEFTEEQKTIKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTNKEPFDVPI"
## [1] "MSQPTWSLQHCALHRANFSHQLVCAIBEYQIBARRBQKWAQAQENNSCBTWWQKTIKIATCLWBQSAABCSTQSQHELMFEBLKMDCPILKNIYTNMQPLNVPI"
## [1] "Total number of residues in original sequence is: 104"
## $Method_A
## $Method_A$`Match Sum`
## [1] 61
## 
## $Method_A$`Match Percentage`
## [1] 58.65385
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 64
## 
## $Method_B$`Match Percentage`
## [1] 61.53846
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 1
## 
## $Method_C$`Match Percentage`
## [1] 0.9615385
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 5
## 
## $Method_D$`Match Percentage`
## [1] 4.807692
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 66
## 
## $Method_E$`Match Percentage`
## [1] 63.46154
## 
## 
## [1] "#################################### bmr15142.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] -0.04081633
## [1] "Method B"
## [1] 0.7142857
## [1] 0.7346939
## [1] "Method C"
## [1] 0.3061224
## [1] -0.08163265
## [1] "Method D"
## [1] 0.5102041
## [1] 0.3673469
## [1] "Method E"
## [1] 0.5102041
## [1] 0.6122449
## [1] "Method A:"
## [1] "MAEVEETLKRLQSQKVQIIVVNTEIPIKSTMDPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE"
## [1] "RAHPWETIKRBQSQMPHIBVMNTHYPFMSTMNPTTTQFASLHKSFIBMAWSTVWDIDPHNLBTBLKIESKKNMIMVAVLRDDFLIVFRNPTW"
## [1] "Method B:"
## [1] "MAEVEETLKRLQSQKVQIIVVNTEIPIKSTMDPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE"
## [1] "WAHVWETBKRBQSQMPHIIVMNTHYPIMSTMNVTTTQIASLHVSFIBWAWSTVWDINPQNLBTLLKIESKKNMIMVAVLRDDFLBVFRNPTE"
## [1] "Method C:"
## [1] "MAEVEETLKRLQSQKVQIIVVNTEIPIKSTMDPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE"
## [1] "VVVCVVVVVVVVVVVVVVVVVVVVCVVVVVVCVVVVVVVVVVVVVVVVVVVVCVVVNVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVV"
## [1] "Method D:"
## [1] "MAEVEETLKRLQSQKVQIIVVNTEIPIKSTMDPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE"
## [1] "CCCCCCCCCCCCCCCCCCCCCNCCCCCCCCMCCCCCQCCCCCCCCCCCCCCCCCCCDCCNCCCCCCCECCCNCCMCCCCCCCCCCCCRNCCC"
## [1] "Method E:"
## [1] "MAEVEETLKRLQSQKVQIIVVNTEIPIKSTMDPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE"
## [1] "WAHVWETBKRBQSQMPHBBVVNTHYPIMSTMNVTTTQIASLRVSFILWAWSTVWDIDPQNLBTLLKIESKKNMIMVAVLRDDFLBVFRNPTE"
## [1] "Total number of residues in original sequence is: 92"
## $Method_A
## $Method_A$`Match Sum`
## [1] 55
## 
## $Method_A$`Match Percentage`
## [1] 59.78261
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 57
## 
## $Method_B$`Match Percentage`
## [1] 61.95652
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 4
## 
## $Method_C$`Match Percentage`
## [1] 4.347826
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 8
## 
## $Method_D$`Match Percentage`
## [1] 8.695652
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 58
## 
## $Method_E$`Match Percentage`
## [1] 63.04348
## 
## 
## [1] "#################################### bmr4851.txt ###################################"

## [1] "Method A"
## [1] 0.1020408
## [1] -2.220446e-16
## [1] "Method B"
## [1] 0.1020408
## [1] 0.08163265
## [1] "Method C"
## [1] 0.1020408
## [1] -0.1632653
## [1] "Method D"
## [1] -0.1020408
## [1] -0.04081633
## [1] "Method E"
## [1] 0.1020408
## [1] 0.1632653
## [1] "Method A:"
## [1] "STDDSPYKQAFSLFDRRIPKTSDLLRAQNPTLAEITEIESTLPAEVDMEQFLQVLNRPFDMDPEEFVFQVFDKDAMELRYVLTSEKLSNEEMDELLVPVKMVNYHDFVQMILA"
## [1] "STDDSPYKQAFSYFNWMYPKTSBFFRAHNPTBAHITEIWSTDPARVNMWQYBQPLNHPFDQNPWWBPYQPFNKDAMQLRYVLTSQWLSNWRMBHLFMPVMQVNYQBFVQMILA"
## [1] "Method B:"
## [1] "STDDSPYKQAFSLFDRRIPKTSDLLRAQNPTLAEITEIESTLPAEVDMEQFLQVLNRPFDMDPEEFVFQVFDKDAMELRYVLTSEKLSNEEMDELLVPVKMVNYHDFVQMILA"
## [1] "STDDSPYKQAISYFNWMYPKTSBBFRAHNPTBAHITEIWSTDVARVNMWQYBQPLNQPFDHNPWWBPYQPFNMDAMQLRYVLTSQELSYWRMBHLFMPVKQVNBWBIVQMYLA"
## [1] "Method C:"
## [1] "STDDSPYKQAFSLFDRRIPKTSDLLRAQNPTLAEITEIESTLPAEVDMEQFLQVLNRPFDMDPEEFVFQVFDKDAMELRYVLTSEKLSNEEMDELLVPVKMVNYHDFVQMILA"
## [1] "VVVCVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCCVVVVVVCVVVVVVVNCVVVCVVVVCVVVVVVVVCVVVVVVVCVVVVVVVVVVVVCVVVVVCVVVVV"
## [1] "Method D:"
## [1] "STDDSPYKQAFSLFDRRIPKTSDLLRAQNPTLAEITEIESTLPAEVDMEQFLQVLNRPFDMDPEEFVFQVFDKDAMELRYVLTSEKLSNEEMDELLVPVKMVNYHDFVQMILA"
## [1] "CCCCCCCCCCCCCCNCMCCCCCCCCCCCNCCCCCCCCCCCCCCCRCCCCQCCCCCCCCCCRCCCCCCCQCCCCCCMQCCCCCCCCCCCCCCCCCCCCCCCQCNCCCCCCCCCC"
## [1] "Method E:"
## [1] "STDDSPYKQAFSLFDRRIPKTSDLLRAQNPTLAEITEIESTLPAEVDMEQFLQVLNRPFDMDPEEFVFQVFDKDAMELRYVLTSEKLSNEEMDELLVPVKMVNYHDFVQMILA"
## [1] "STDDSPYKQAISYFNWMYPKTSBBFRAHNPTLAHITEIWSTDVARVDMWQYBQPLNQPFDHNPWWBPYQPFNMDAMQLRYVLTSQELSNWRMBHLFKPVKQVNYQBFVQMYLA"
## [1] "Total number of residues in original sequence is: 113"
## $Method_A
## $Method_A$`Match Sum`
## [1] 71
## 
## $Method_A$`Match Percentage`
## [1] 62.83186
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 65
## 
## $Method_B$`Match Percentage`
## [1] 57.52212
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 3
## 
## $Method_C$`Match Percentage`
## [1] 2.654867
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 5
## 
## $Method_D$`Match Percentage`
## [1] 4.424779
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 70
## 
## $Method_E$`Match Percentage`
## [1] 61.9469
## 
## 
## [1] "#################################### bmr4858.txt ###################################"

## [1] "Method A"
## [1] 1.530612
## [1] 1.510204
## [1] "Method B"
## [1] 1.734694
## [1] 1.714286
## [1] "Method C"
## [1] 0.7142857
## [1] 0.6938776
## [1] "Method D"
## [1] 0.7142857
## [1] 0.6530612
## [1] "Method E"
## [1] 2.142857
## [1] 2.163265
## [1] "Method A:"
## [1] "SHMLEDPVESESTTPFNLFINLNPNKSVAELKVAISELFAKNDLAVVDVRTTNRKFYVDFESAEDLEKALELTLKVFNEIKLEKPKRDTRC"
## [1] "SEKBEDPPWSESTTPNDLBBNLNPNHSVARBVVAISWBIAKDBLAVPLIRTTNRMLBVDBRSAWFBEKALRFTBMPYNCFKLKKPKRDTWB"
## [1] "Method B:"
## [1] "SHMLEDPVESESTTPFNLFINLNPNKSVAELKVAISELFAKNDLAVVDVRTTNRKFYVDFESAEDLEKALELTLKVFNEIKLEKPKRDTRC"
## [1] "SEKBEDPPESESTTPNDLBBNLNPNHSVARLVVAISWLIAKDBLAVPLVRTTNRMLBVDLRSAWBLWKALEBTBMVBNCIKLKKPKRDTEB"
## [1] "Method C:"
## [1] "SHMLEDPVESESTTPFNLFINLNPNKSVAELKVAISELFAKNDLAVVDVRTTNRKFYVDFESAEDLEKALELTLKVFNEIKLEKPKRDTRC"
## [1] "VVVVVCCCVVVVVVVVVVVVVVVCVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVVVVCVVVVVVVVVVVVVVVVVCVVVVVVVVVVVVVVV"
## [1] "Method D:"
## [1] "SHMLEDPVESESTTPFNLFINLNPNKSVAELKVAISELFAKNDLAVVDVRTTNRKFYVDFESAEDLEKALELTLKVFNEIKLEKPKRDTRC"
## [1] "CCCCCCCCCCCCCCCCCCCCCCNCCQCCCCCCCCCCCCCCCCCCCCCCCRCCCCCCCCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCC"
## [1] "Method E:"
## [1] "SHMLEDPVESESTTPFNLFINLNPNKSVAELKVAISELFAKNDLAVVDVRTTNRKFYVDFESAEDLEKALELTLKVFNEIKLEKPKRDTRC"
## [1] "SEKBEDPPESESTTPNDLBLNLNPNHSVARLVVAISWLIAKDBLAVPLVRTTNRMLBVDLRSAWBLEKALEBTBMVYNCFMLKKPKRDTEB"
## [1] "Total number of residues in original sequence is: 91"
## $Method_A
## $Method_A$`Match Sum`
## [1] 51
## 
## $Method_A$`Match Percentage`
## [1] 56.04396
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 58
## 
## $Method_B$`Match Percentage`
## [1] 63.73626
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 4
## 
## $Method_C$`Match Percentage`
## [1] 4.395604
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 4
## 
## $Method_D$`Match Percentage`
## [1] 4.395604
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 57
## 
## $Method_E$`Match Percentage`
## [1] 62.63736
## 
## 
## [1] "#################################### bmr5200.txt ###################################"

## [1] "Method A"
## [1] 0.3061224
## [1] 0.2040816
## [1] "Method B"
## [1] 0.3061224
## [1] 0.3673469
## [1] "Method C"
## [1] 0.5102041
## [1] 0.4081633
## [1] "Method D"
## [1] 0.5102041
## [1] 0.4897959
## [1] "Method E"
## [1] 0.7142857
## [1] 0.7346939
## [1] "Method A:"
## [1] "VTIDNIQKTVAEYYKIKVADLLSKRRSSVARPRQMAMALAKELTNHSLPEIDAFRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS"
## [1] "VTIBNICKTVAHFYCIMVABLFSKMRSSVACPPCMAVALAMRBTNESFVRILANEDRTTVBRACRRVYMBREMSWBIPQBFSNLIWTBSS"
## [1] "Method B:"
## [1] "VTIDNIQKTVAEYYKIKVADLLSKRRSSVARPRQMAMALAKELTNHSLPEIDAFRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS"
## [1] "VTIBNICKTVAHIBCBMVABLBSKMRSSVACPVCMAVALAMRBTNESFVRILAYEDRTTPLRACRMVBMLREMSWBVVQBISNLIWTBSS"
## [1] "Method C:"
## [1] "VTIDNIQKTVAEYYKIKVADLLSKRRSSVARPRQMAMALAKELTNHSLPEIDAFRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS"
## [1] "VVVVCVVVVCVVVCVVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVCVVVVVCVVVVVVCCVVVVVVVVVVVVVVCVVVVVVV"
## [1] "Method D:"
## [1] "VTIDNIQKTVAEYYKIKVADLLSKRRSSVARPRQMAMALAKELTNHSLPEIDAFRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS"
## [1] "CCCCCCCCCCCCCCCCMCCCCCCCCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCCCCCC"
## [1] "Method E:"
## [1] "VTIDNIQKTVAEYYKIKVADLLSKRRSSVARPRQMAMALAKELTNHSLPEIDAFRDHTTVLHACRKIEQLREESHDIKEDFSNLIRTLSS"
## [1] "VTIBNICKTVAHIBCBMVABLFSKMRSSVACVVCMAVALAMRBTNESFVRILANEDRTTVLRACRMVYMLREMSWBVVQLISNLIWTBSS"
## [1] "Total number of residues in original sequence is: 90"
## $Method_A
## $Method_A$`Match Sum`
## [1] 51
## 
## $Method_A$`Match Percentage`
## [1] 56.66667
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 48
## 
## $Method_B$`Match Percentage`
## [1] 53.33333
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 2
## 
## $Method_C$`Match Percentage`
## [1] 2.222222
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 2
## 
## $Method_D$`Match Percentage`
## [1] 2.222222
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 48
## 
## $Method_E$`Match Percentage`
## [1] 53.33333
## 
## 
## [1] "#################################### bmr5402.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] 0
## [1] "Method B"
## [1] -0.1020408
## [1] -0.08163265
## [1] "Method C"
## [1] -0.3061224
## [1] -0.4081633
## [1] "Method D"
## [1] 0.5102041
## [1] 0.4897959
## [1] "Method E"
## [1] -0.1020408
## [1] -0.122449
## [1] "Method A:"
## [1] "TEAEDSIEMYEWYSKHMTRSQAEQLLKQEKEFIVRDSSKAKYTVSVAKSTDPQVIHYVVCSTPQSQYYAEKHLFSTPELNYHQHNSRLKYPVSQQNKNA"
## [1] "TCACDSIQQYCHNSKHMTWSQAWQLLKQQRCBBPRDSSHARYTKSVAMSTNIQVIQDPCQSTPHSHBBAWRHLBSTPRLYIQRRNSMBMDPPSQQNWNA"
## [1] "Method B:"
## [1] "TEAEDSIEMYEWYSKHMTRSQAEQLLKQEKEFIVRDSSKAKYTVSVAKSTDPQVIHYVVCSTPQSQYYAEKHLFSTPELNYHQHNSRLKYPVSQQNKNA"
## [1] "TCACDSIQQYCQNSKQMTWSQAWQLLKQQRCBBVMDSSHARYTVSVAMSTNIQVBQDPCQSTPQSQBBAWRHLBSTPRLYIQERNSKBVDVVSQQNWNA"
## [1] "Method C:"
## [1] "TEAEDSIEMYEWYSKHMTRSQAEQLLKQEKEFIVRDSSKAKYTVSVAKSTDPQVIHYVVCSTPQSQYYAEKHLFSTPELNYHQHNSRLKYPVSQQNKNA"
## [1] "VVVVCVVVVCVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVNVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVNVVVVCVVVVVVVVV"
## [1] "Method D:"
## [1] "TEAEDSIEMYEWYSKHMTRSQAEQLLKQEKEFIVRDSSKAKYTVSVAKSTDPQVIHYVVCSTPQSQYYAEKHLFSTPELNYHQHNSRLKYPVSQQNKNA"
## [1] "CCCCCCCCQCCCCCCCCCCCQCWCCCCCCRCCCCMCCCHCRCCCCCCCCCCCCCCQCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCNCNC"
## [1] "Method E:"
## [1] "TEAEDSIEMYEWYSKHMTRSQAEQLLKQEKEFIVRDSSKAKYTVSVAKSTDPQVIHYVVCSTPQSQYYAEKHLFSTPELNYHQHNSRLKYPVSQQNKNA"
## [1] "TCACDSYQQYCQNSKQMTWSQAWQLLKQQMQBLVMDSSHAMYTVSVAMSTNIQVBQDPCQSTPQSQBBAWRHLBSTVRLYIQERNSKBVDVVSQQNWNA"
## [1] "Total number of residues in original sequence is: 99"
## $Method_A
## $Method_A$`Match Sum`
## [1] 54
## 
## $Method_A$`Match Percentage`
## [1] 54.54545
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 55
## 
## $Method_B$`Match Percentage`
## [1] 55.55556
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 7
## 
## $Method_C$`Match Percentage`
## [1] 7.070707
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 4
## 
## $Method_D$`Match Percentage`
## [1] 4.040404
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 53
## 
## $Method_E$`Match Percentage`
## [1] 53.53535
## 
## 
## [1] "#################################### bmr6693.txt ###################################"

## [1] "Method A"
## [1] 0.1020408
## [1] 0.122449
## [1] "Method B"
## [1] 0.1020408
## [1] 0.04081633
## [1] "Method C"
## [1] 0.1020408
## [1] 0.2857143
## [1] "Method D"
## [1] 0.1020408
## [1] 0.1632653
## [1] "Method E"
## [1] 0.1020408
## [1] 0.08163265
## [1] "Method A:"
## [1] "TTAYQPIACATTQSEAAAYQKRWLVANAQWLNRDLCPRLAEVSVELMYLVLKPMLRLDIPLDVIEDDDSVRYQMVEQTVDVVEELAAAWISNAVPCRILKVHPDMAEVRWPS"
## [1] "TTAYHPYAQASTRSEAAAFCRHMLVANAHQDNRBBQPHFARPSVMLWLDVLNPMLWDNBPFDVYCDDDSPRBHMPHQTVDYVCRBAAAPISNAMPEMILMPMPDQARVHHPS"
## [1] "Method B:"
## [1] "TTAYQPIACATTQSEAAAYQKRWLVANAQWLNRDLCPRLAEVSVELMYLVLKPMLRLDIPLDVIEDDDSVRYQMVEQTVDVVEELAAAWISNAVPCRILKVHPDMAEVRWPS"
## [1] "TTAYHPYAQATTRSEAAAFCRHKBVANAHCDNRDBQPHFARPSVMLRLDVLNPMLWDNBPFDVYCDDDSPRNHMPHQTVDYVCRBAAAPISNAKPEKILMPMPDQARVHQPS"
## [1] "Method C:"
## [1] "TTAYQPIACATTQSEAAAYQKRWLVANAQWLNRDLCPRLAEVSVELMYLVLKPMLRLDIPLDVIEDDDSVRYQMVEQTVDVVEELAAAWISNAVPCRILKVHPDMAEVRWPS"
## [1] "VVVVVCCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVCVVVVVVVVVVVVVCVVVVVVVVVVVVVCVVVVVVCVCCVVVVVVVVVCVVVVVVVVVVCVVVVVVVVV"
## [1] "Method D:"
## [1] "TTAYQPIACATTQSEAAAYQKRWLVANAQWLNRDLCPRLAEVSVELMYLVLKPMLRLDIPLDVIEDDDSVRYQMVEQTVDVVEELAAAWISNAVPCRILKVHPDMAEVRWPS"
## [1] "CCCCQCCCCCCCCCCCCCCCCCCCCCNCCCCNCCCCCCCCRCCCMCCCCCCCCMCCCCCCCCCCCCCCCCRCHCCCQCCCCCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCC"
## [1] "Method E:"
## [1] "TTAYQPIACATTQSEAAAYQKRWLVANAQWLNRDLCPRLAEVSVELMYLVLKPMLRLDIPLDVIEDDDSVRYQMVEQTVDVVEELAAAWISNAVPCRILKVHPDMAEVRWPS"
## [1] "TTAYHPYAQATTRSEAAAFCRQKLVANAHCDNRDBQPHFARPSVMLRLDVLNPMLWDDBPFDVYCDDDSPRNHMPHQTVDYVCRLAAAVISNAKPEKILMPMPDQARVQQPS"
## [1] "Total number of residues in original sequence is: 112"
## $Method_A
## $Method_A$`Match Sum`
## [1] 60
## 
## $Method_A$`Match Percentage`
## [1] 53.57143
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 61
## 
## $Method_B$`Match Percentage`
## [1] 54.46429
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 9
## 
## $Method_C$`Match Percentage`
## [1] 8.035714
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 9
## 
## $Method_D$`Match Percentage`
## [1] 8.035714
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 64
## 
## $Method_E$`Match Percentage`
## [1] 57.14286
## 
## 
## [1] "#################################### bmr7121.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] -0.1632653
## [1] "Method B"
## [1] -0.1020408
## [1] -0.08163265
## [1] "Method C"
## [1] -0.5102041
## [1] -0.2040816
## [1] "Method D"
## [1] -0.5102041
## [1] -0.4489796
## [1] "Method E"
## [1] -0.1020408
## [1] 0
## [1] "Method A:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBLHBHBYMWRMNBTKBBNSPTNLSVLEBBTWMNHAQDCHPDPPNQNBYVRSWTDQHYTQSFRPTBLBTLTTMPBDSTQTAPRRYBVHHSTVHPEHYCQRIAQMYMDLSCADNQTBLWFHRANHWYYDPAM"
## [1] "Method B:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBLQBCBFVWRMNBTKBBNTPTNLSVBEBBTWMDHAQDCQPDPVNQNBYVRSWTDQHYTQSFEPTDLBTLTTMPBDSTCTAVRMYIVHQSTVHPWHYCQRIAQMYMLLSCADNQTBLWFHRANEWYYDPAK"
## [1] "Method C:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "VVNVVVVVVVVVVVVVVVVVVVVNVVVCVVCVVVVVVVCVVVCVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVCVVVVVVVCVVVVVVVVVCVVVVVVVV"
## [1] "Method D:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "CRNCCCCCCCCCCCCRCNCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCCCQNCCCRCCCCQCCCCCCCCCCCCCCCCCCCCCCCCCCCMCCCCCCCCCCECCCCCCCCCCMCCCCCCCCCCCCCCCCCCCCCCCCC"
## [1] "Method E:"
## [1] "LKFIEYFDRTVIYICEHNDTVIINTPTDLSVLELLTRMDMAQDQMVLPVNQDFIVHSKTDHEFTHSYKVTDDITLTTDVLDSTQTAPEKFIVCCSTWKPHQLEQEIAQNYWLLSEANNQTLFEYVEANEMIILRAL"
## [1] "DRNBRYBFQBCYFVWRMNDTMBBNTPTNLSVLELBTWMNHAQDCQPDPVNQNBYVRSWTDQHYTQSFEVTDLBTLTTNPBDSTQTAVRMYIVHHSTVHVWHYCQRIAQMYMLLSCADNQTBLWFHKANEWYYDPAM"
## [1] "Total number of residues in original sequence is: 136"
## $Method_A
## $Method_A$`Match Sum`
## [1] 56
## 
## $Method_A$`Match Percentage`
## [1] 41.17647
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 59
## 
## $Method_B$`Match Percentage`
## [1] 43.38235
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 9
## 
## $Method_C$`Match Percentage`
## [1] 6.617647
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 6
## 
## $Method_D$`Match Percentage`
## [1] 4.411765
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 62
## 
## $Method_E$`Match Percentage`
## [1] 45.58824
## 
## 
## [1] "#################################### bmr7376.txt ###################################"

## [1] "Method A"
## [1] -0.1020408
## [1] -0.04081633
## [1] "Method B"
## [1] -0.1020408
## [1] -0.08163265
## [1] "Method C"
## [1] 0.1020408
## [1] 0.122449
## [1] "Method D"
## [1] -0.7142857
## [1] 0.2857143
## [1] "Method E"
## [1] 0.3061224
## [1] 0.3265306
## [1] "Method A:"
## [1] "AEQYSEINTDTLEREIFKADYNRIRIMELLSVSEASHISHQLNLSQSHQLKLLKSVKAKRQSMIYSLDDIHVATMLKQAIHHANHPKE"
## [1] "AEHYSCYNTDTFWREIYKALFNEPRIBQILSPSQASRISQQDMLSCSEQBKLLKSBMAMHQSRBLSYBNBRVATVLKQAIQWANHPMC"
## [1] "Method B:"
## [1] "AEQYSEINTDTLEREIFKADYNRIRIMELLSVSEASHISHQLNLSQSHQLKLLKSVKAKRQSMIYSLDDIHVATMLKQAIHHANHPKE"
## [1] "AEHYSCYNTDTBWREIYKALFNEVRIYQBBSPSQASRISQQDMLSCSEQBKLLKSKMAMRQSRYLSFBNBRVATVLKQAIQWANQPMC"
## [1] "Method C:"
## [1] "AEQYSEINTDTLEREIFKADYNRIRIMELLSVSEASHISHQLNLSQSHQLKLLKSVKAKRQSMIYSLDDIHVATMLKQAIHHANHPKE"
## [1] "VVVCVVVVVVVVVVVVVVVVVCVCVVVVVVVCVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVCVVVVVVVVVVVNVVVV"
## [1] "Method D:"
## [1] "AEQYSEINTDTLEREIFKADYNRIRIMELLSVSEASHISHQLNLSQSHQLKLLKSVKAKRQSMIYSLDDIHVATMLKQAIHHANHPKE"
## [1] "CCCCCCCNCCCCWCCCCCCCCCCCCCCCCCCCCCCCCCCCQCCCCCCCCCCCCCCCCCMCCCRCCCCCNCCCCCCCCCCCCCCCCCCC"
## [1] "Method E:"
## [1] "AEQYSEINTDTLEREIFKADYNRIRIMELLSVSEASHISHQLNLSQSHQLKLLKSVKAKRQSMIYSLDDIHVATMLKQAIHHANHPKE"
## [1] "AEHYSCYNTDTBWREIYKALFNEVRIYQLFSPSQASRISQQDMLSCSEQBKLLKSKMAMRQSRYLSFBNBRVATVLKQAIQWANQPMC"
## [1] "Total number of residues in original sequence is: 88"
## $Method_A
## $Method_A$`Match Sum`
## [1] 49
## 
## $Method_A$`Match Percentage`
## [1] 55.68182
## 
## 
## $Method_B
## $Method_B$`Match Sum`
## [1] 48
## 
## $Method_B$`Match Percentage`
## [1] 54.54545
## 
## 
## $Method_C
## $Method_C$`Match Sum`
## [1] 2
## 
## $Method_C$`Match Percentage`
## [1] 2.272727
## 
## 
## $Method_D
## $Method_D$`Match Sum`
## [1] 2
## 
## $Method_D$`Match Percentage`
## [1] 2.272727
## 
## 
## $Method_E
## $Method_E$`Match Sum`
## [1] 49
## 
## $Method_E$`Match Percentage`
## [1] 55.68182

NMRref

Xi Chen

2016-01-26